rs2256038

Positions:

• chr21-15148855-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.497 in 152,032 control chromosomes in the GnomAD database, including 22,008 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (22008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75370 AN: 151914 Hom.: 21921 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.497 AC: 75533 AN: 152032 Hom.: 22008 Cov.: 32 AF XY: 0.499 AC XY: 37123 AN XY: 74330

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.475

Alfa AF: 0.370 Hom.: 11147

Bravo AF: 0.519

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2256038; hg19: chr21-16521176;